# Dynamical Systems Approach to Immune Response Modeling

## Documentation for package ‘DSAIRM’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

check_simresults | A function that checks if a call to simulation function worked
dsairmmenu | The main menu for the DSAIRM package
generate_documentation | A helper function which processes and displays the documentation part for each app
generate_fctcall | A helper function that produces a call to a simulator function for specific settings
generate_ggplot | A helper function that takes simulation results and produces ggplot plots
generate_modelsettings | A function to parse modelsettings for simulation runs
generate_plotly | A helper function that takes simulation results and produces plotly plots
generate_shinyinput | A helper function that takes a model and generates shiny UI elements
generate_text | A helper function that takes result from the simulators and produces text output
hayden96flu | Influenza virus load data
run_model | A function that runs an app for specific settings and processes results for plot and text generation
schirm20strep | Streptococcus pneumoniae infection data
simulate_acutevirusir_ode | Acute Virus Infection and IR Model
simulate_bacteria_fit | Fitting a simple bacteria infection models to Streptococcus pneumoniae infection data
simulate_basicbacteria_discrete | Basic Bacteria model - discrete
simulate_basicbacteria_modelexploration | Simulation to illustrate parameter scan of the basic bacteria model #'
simulate_basicbacteria_ode | Basic Bacteria model - ODE
simulate_basicvirus_fit | Fitting a simple viral infection models to influenza data
simulate_basicvirus_modelexploration | Simulation to illustrate parameter scan of the basic virus model #'
simulate_basicvirus_ode | Basic Virus Model
simulate_basicvirus_stochastic | Basic Virus Model
simulate_chronicvirusir_ode | Chronic Virus Infection and IR Model
simulate_confint_fit | Fit a simple viral infection model and compute confidence intervals
simulate_drugresistance_stochastic | Stochastic simulation of a compartmental acute virus infection model with treatment and drug resistant strain
simulate_extendedbacteria_ode | Extended Bacteria model - ODE
simulate_fludrug_fit | Fitting a simple viral infection model with 2 types of drug mechanisms to influenza data
simulate_modelcomparison_fit | Fitting 2 simple viral infection models to influenza data
simulate_modelvariants_ode | Simulation of a viral infection model with immune response The simulation illustrates different alternative models.
simulate_pkpdmodel_ode | PkPd Virus model
simulate_usanalysis | Simulation to illustrate uncertainty and sensitivity analysis
simulate_virusandir_ode | Simulation of a viral infection model with an immune response
simulate_virusandtx_ode | Simulation of a basic viral infection model with drug treatment